hotspotter.variable: Find hotspots of genomic events

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Find hotspots of genomic events

Description

Find hotspots of genomic events by using kernel density estimation.

Usage

hotspotter.variable(breakpoints, confint, pval = 0.05, spacing.bp = 5000)

Arguments

breakpoints	A list with GRanges-class object containing the coordinates of the genomic events and their confidence intervals.
confint	Confidence interval that was used for breakpoint estimation.
pval	P-value cutoff for hotspots.
spacing.bp	Spacing of datapoints for KDE in basepairs.

Details

The hotspotter uses a gaussian kernel with variable bandwidth to perform a KDE. The bandwidth depends on the confidence intervals of the breakpoints. A p-value is calculated by comparing the density profile of the genomic events with the density profile of a randomly subsampled set of genomic events (bootstrapping).

Value

A list of GRanges-class objects containing 1) coordinates of hotspots and 2) p-values within the hotspot.

Author(s)

Aaron Taudt

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.